NM_000466.3(PEX1):c.1108del (p.Ile370fs) AND Zellweger syndrome

Clinical significance:Pathogenic (Last evaluated: Mar 28, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001210281.2

Allele description [Variation Report for NM_000466.3(PEX1):c.1108del (p.Ile370fs)]

NM_000466.3(PEX1):c.1108del (p.Ile370fs)

Gene:
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_000466.3(PEX1):c.1108del (p.Ile370fs)
HGVS:
  • NC_000007.13:g.92146721del
  • NC_000007.14:g.92517415del
  • NG_008341.1:g.16125del
  • NG_008341.2:g.16125del
  • NM_000466.3:c.1108delMANE SELECT
  • NM_001282677.2:c.1108del
  • NM_001282678.2:c.484del
  • NP_000457.1:p.Ile370fs
  • NP_001269606.1:p.Ile370fs
  • NP_001269607.1:p.Ile162fs
  • NC_000007.13:g.92146721del
  • NC_000007.13:g.92146729del
  • NC_000007.13:g.92146729delT
  • NM_000466.2:c.1108del
  • NM_000466.2:c.1108delA
Protein change:
I162fs
Links:
dbSNP: rs61750406
NCBI 1000 Genomes Browser:
rs61750406
Molecular consequence:
  • NM_000466.3:c.1108del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282677.2:c.1108del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282678.2:c.484del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Zellweger syndrome (ZS)
Synonyms:
Zellweger spectrum disorders
Identifiers:
MONDO: MONDO:0019609; MedGen: C0043459; Orphanet: 912

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001381760Invitaecriteria provided, single submitter
Pathogenic
(Mar 28, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in PEX1 are the most common cause of peroxisome biogenesis disorders.

Reuber BE, Germain-Lee E, Collins CS, Morrell JC, Ameritunga R, Moser HW, Valle D, Gould SJ.

Nat Genet. 1997 Dec;17(4):445-8.

PubMed [citation]
PMID:
9398847

PEX1 mutations in the Zellweger spectrum of the peroxisome biogenesis disorders.

Crane DI, Maxwell MA, Paton BC.

Hum Mutat. 2005 Sep;26(3):167-75. Review.

PubMed [citation]
PMID:
16086329
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001381760.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Ile370Leufs*17) in the PEX1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs755998864, ExAC 0.5%). This variant has not been reported in the literature in individuals with PEX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 371779). Loss-of-function variants in PEX1 are known to be pathogenic (PMID: 9398847, 16086329, 16141001, 21031596). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2021

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